<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">

<HTML>
    <HEAD>
        <TITLE></TITLE>
    </HEAD>
    <BODY>
        <a name="#top"/>
        <H2>OLSDialog</H2>
        <p align="justify">  
            The OLS Dialog is an easy and straightforward way of interacting
            with the Ontology Lookup Service (OLS). More information about the
            OLS can be found <a href="http://www.ebi.ac.uk/ontology-lookup">here</a>.
            More details about the OLS Dialog can be found at the project web page:
            <a href="http://ols-dialog.googlecode.com">http://ols-dialog.googlecode.com</a>.
            <br><br>
            There are five ways of searching the OLS using the OLS Dialog:
        </p>

        <ul>
            <li><a href='#termNameSearch'>Term Name Search</a></li>
            <li><a href='#termIdSearch'>Term ID Search</a></li>
            <li><a href='#massSearch'>PSI-MOD Mass Search</a></li>
            <li><a href='#browseOntology'>Browse Ontology</a></li>
            <li><a href='#termHierarcy'>Term Hierarcy Graph</a></li>
        </ul>

        <p align="justify">
            For all search types the ontology to search in is selected at the top.
            However, for PSI-MOD Mass Search the ontology is always set to PSI-MOD
            has the PSI-MOD Mass Search is created with this specific ontology in mind.
        </p>
        <br>
        <a href="#top">Go to top of page</a><br><br>

        <a name='#termNameSearch'></a>
        <H3>Term Name Search</H3>
        <p align="justify">
            Term Name Search simply finds all term names that (partially) match the insert
            search term. Insert the first letters of the term to locate
            in the search field. Note that the search is in "real time". Meaning that a new
            search is started (and the result list updated) for every character
            typed. The number behind the search field is the number of currently
            matching terms.
            <br><br>
            Note that in some cases a complete search is not performed until at least four
            characters have been inserted. If the wanted term is not found, make sure
            that at least four characters have been inserted.
            <br><br>
            The search results are listed in the table in the middle, and
            clicking a term displays additional information about the selected term
            in the "Term Details" section below.
            <br><br>
            When the wanted term has been found, select the term in the table
            and click the "Use Selected Term" button at the bottom of the frame.
            (Or you can double click on the selected term.)
        </p>
        <br>
        <a href="#top">Go to top of page</a><br><br>

        <a name='#termIdSearch'></a>
        <H3>Term ID Search</H3>
        <p align="justify">
            Term ID Search allows you the locate a given term and its details by 
            inserting the term id, e.g., MOD:00425 or GO:0000269.
            <br><br>
            The results are displayed and selected in the same way as for results 
            from a <a href='#termNameSearch'>Term Name Search</a>.
        </p>
        <br>
        <a href="#top">Go to top of page</a><br><br>

        <a name='#massSearch'></a>
        <H3>PSI-MOD Mass Search</H3>
        <p align="justify">
            PSI-MOD Mass Search allows you to search the PSI-MOD ontology for specific
            modifications using the mass of the modification. There are four
            different mass types: DiffAvg and DiffMono corresponding to the
            average and mono mass of the mass change the modifications results
            in, and MassAvg and MassMono corresponding to the mass of the
            modified residue.
            <br><br>
            Insert the mass, the mass accuracy and the mass type and click on
            "Search" to perform the search. The results are displayed and selected
            in the same way as for results from a <a href='#termNameSearch'>Term Name Search</a>.
        </p>
        <br>
        <a href="#top">Go to top of page</a><br><br>

        <a name='#browseOntology'></a>
        <H3>Browse Ontology</H3>
        <p align="justify">
            Browse Ontology makes it possible to find the wanted term by
            browsing the selected ontology. The ontology is displayed using
            a tree structure where the relationships between the terms are
            highlighted. When selecting a term in the tree, details about
            the selected term is displayed in the "Term Details" section.
            <br><br>
            The results are selected and used in the same way as for results 
            from a <a href='#termNameSearch'>Term Name Search</a>.
        </p>
        <BR>
        <a href="#top">Go to top of page</a><br><br>

        <a name='#termHierarcy'></a>
        <H3>Term Hierarcy Graph</H3>
        <p align="justify">
            In addition to the four general search options, it is also possible
            to view the term hierarcy of a selected term. When a term is selected
            simply click the View Term Hierarcy link on top and to the right of
            the selected terms definition text area. This will display the selected
            terms term hierarcy as a directed acyclic graph.
        </p>
        <BR>
        <a href="#top">Go to top of page</a><br>

    </BODY>
</HTML>